A reduction in blood flow and tissue perfusion is particularly damaging to the heart once the tissue is subsequently reperfused by warm, oxygenated blood. Remarkably, this ischemia/reperfusion injury is not observed in organs of hibernating animals after emerging from hibernation and establishing a normal heart rate and body temperature. The thirteen-lined ground squirrel (Spermophilus tridecemlineatus) is a hibernating mammal that provides a critical perspective into the molecular basis of heart function under extreme physiological conditions. However, molecular analysis of any hibernating species is complicated by the intractability of classical genetics and the lack of a sequenced genome. In order to address this issue, we have undertaken a high-throughput cDNA sequencing project designed to compare the transcriptomes of both active and hibernating hearts. Over 4000 heart cDNAs from both active and hibernating animals will be sequenced and characterized for this assay. Genes that are found to be significantly up or down-regulated during hibernation based on this approach will be subjected to real time RT-PCR quantification of mRNA levels to validate our results. Groups of functionally similar gene products will be analyzed for the generalized up or down-regulation of cellular processes during the hibernating state Differentially regulated genes encoding proteins involved in rate-limiting catalysis, key regulatory steps, or novel enzymatic activities will be directly quantified by immunoblotting and/or activity assays. The sequencing and characterization of ground squirrel heart cDNA libraries will serve as markers for a future thirteen-lined ground squirrel genome project and create a substantial wealth of information by providing species-specific sequence data for subsequent hibernation studies.